Variant report

Variant	rs11671540
Chromosome Location	chr19:18512157-18512158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZC3H11A	chr19:18511989-18512180	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18494076..18504244-chr19:18508099..18514509,16	MCF-7	breast:
2	chr19:18506537..18511375-chr19:18511397..18514824,5	K562	blood:
3	chr19:18390571..18392343-chr19:18511701..18513366,2	K562	blood:
4	chr19:18451491..18453396-chr19:18510638..18513266,2	K562	blood:
5	chr19:18390843..18392490-chr19:18510995..18513201,2	K562	blood:

No data

Variant related genes	Relation type
LRRC25	TF binding region
ENSG00000175489	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000130522	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1002640	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421074	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10424080	0.86[ASN][1000 genomes]
rs11086108	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12971295	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13344313	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2888142	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35336015	0.80[ASN][1000 genomes]
rs4808800	0.87[ASN][1000 genomes]
rs8112969	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9749546	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
9	nsv2430	chr19:18496428-18514937	Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
10	nsv911276	chr19:18497141-18554972	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18508400-18525400	Weak transcription	Right Atrium	heart
2	chr19:18508600-18512400	Weak transcription	Lung	lung
3	chr19:18508800-18514400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:18508800-18514800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:18508800-18525200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr19:18509000-18512400	Weak transcription	Fetal Intestine Large	intestine
7	chr19:18509000-18512800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:18509000-18515200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr19:18509200-18512400	Weak transcription	Fetal Intestine Small	intestine
10	chr19:18509400-18512200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr19:18509400-18512400	Weak transcription	Spleen	Spleen
12	chr19:18509400-18512600	Weak transcription	Gastric	stomach
13	chr19:18510000-18512800	Weak transcription	Liver	Liver
14	chr19:18510200-18512200	Weak transcription	Placenta	Placenta
15	chr19:18510200-18512400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:18510200-18512600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:18510200-18512600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:18510200-18512800	Weak transcription	Colonic Mucosa	Colon
19	chr19:18510200-18512800	Weak transcription	Ovary	ovary
20	chr19:18510200-18512800	Weak transcription	Stomach Mucosa	stomach
21	chr19:18510400-18512400	Weak transcription	HepG2	liver
22	chr19:18510400-18512600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:18510800-18513000	Enhancers	Hela-S3	cervix
24	chr19:18511000-18512200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:18511000-18513000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:18511000-18513200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:18511400-18512600	Enhancers	Primary B cells from cord blood	blood
28	chr19:18511600-18512400	Enhancers	GM12878-XiMat	blood
29	chr19:18511600-18512800	Enhancers	A549	lung
30	chr19:18511600-18513200	Enhancers	Fetal Thymus	thymus
31	chr19:18511600-18514800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr19:18511600-18515200	Enhancers	Primary hematopoietic stem cells	blood
33	chr19:18511600-18515200	Enhancers	Fetal Muscle Leg	muscle
34	chr19:18511800-18512200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:18511800-18512200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:18511800-18512200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr19:18511800-18512200	Weak transcription	K562	blood
38	chr19:18511800-18512600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:18511800-18512800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:18511800-18512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:18511800-18512800	Weak transcription	NHDF-Ad	bronchial
42	chr19:18511800-18512800	Weak transcription	NHEK	skin
43	chr19:18511800-18512800	Weak transcription	NHLF	lung
44	chr19:18512000-18512200	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr19:18512000-18515800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links